Hi all,
I noticed something while reviewing the data for one of my samples (49915_2_156
), which is paired-end and contains no singleton reads. I ran it through MetaPhlAn 4.0.6using the -t rel_ab_w_read_stats
option and the updated 2024 MetaPhlAn database(#mpa_vJun23_CHOCOPhlAnSGB_202403).
The MetaPhlAn output reports that 137,492 reads were processed, yet the estimated read counts mapped/unmapped to taxa sum to 1,554,273 for this sample.
I was expecting these numbers to be closer. Does MetaPhlAn count individual reads (rather than read pairs), and is it normal for the estimated read count to significantly exceed the number of processed reads? I’d really appreciate an explanation for this disparity between the input and output read counts.
Thanks in advance!
Uzma